Regarding Program Punishments, author's have pretty much explored the range of it, or simply ignored it. Although the BDSM side doesn't tend to show up very often, unlike in Karen's initial opening story.
Beyond that, dystopian and/or hedonistic tends to be favored. They almost all tend to point out and play out the fact that the Programs stated goals, and its methods seem to often be at odds with each other.
Although sometimes you'll see the nudist rather than hedonist take turn up, but those are very rare. When the "nudist view" or perspective does turn up, it's usually to point out the cross-purposes the Program is working towards. As part of its initial stated purpose and objective reads like something most Nudists would support, or even write. Up until you get to the forced nudity, and you certainly lose most (strict) nudists once you start getting into public displays of sexuality. (The hedonists are another matter) As most nudists go to great lengths to try to disconnect the two concepts from each other, while NiS is almost attempting to weld them together permanently.
2] It really does seem to me that the idea of the Progrm [according to most stories] was/is to make most girls into sluts. To force them to experience the 'joys of being a slut', so that many of them would decide that slutdum is a good way to live if there are no STD and babies as a result. The original story by Karen Wagner assumed that most girls are really submissives at heart and just need a nudge for them up to wake up to that fact. [Not true of course, except for 5% to 10% of girls.] Other stories later just assumed most girls are natural sluts.
I don't know about all of them being submissive, even in Karen's take. You also have to keep in mind that in a school situation, the students are in an inherently submissive situation in regards to the teachers in the first place. So even if the specific person in question isn't normally submissive, they're going to have to bend a little in regards to what the teachers want in many cases.
But yes, in the Wagner-verse, it is full on sexual liberation and pushing of boundaries as well as comfort zones for the female students in particular. It's very much putting hedonism on a scale of 1 to 10, and dialing it up to 11.
It also is inherently sexist, and that kind of was the point, I believe. After a person turns 21, only women are allowed to continue being nude in Public. (Objectification of the female form) Accounts of women using their sexuality and "feminine wiles" to "get their way" on various things(sexual politics, more female objectification), only boys being allowed to get relief in class because of "blue balls"(which later iterations of NiS stories made more "equal opportunity"so the girls could get relief as well. Again, at least until it was "equalized" the boys sexual needs were paramount, the girls "didn't matter"). and so forth.
As to the "natural sluts" I think a lot of that goes to what a person wants to define as being "slutty" and some set a higher bar than others. Within the context of Reality, I would tend to believe that there is a very large number (of most devoutly religious) women who literally have no idea what good sex is. Because they've never had it.
They've been socially conditioned to not (directly/clearly) communicate their wants and desires to their (male) sex partners, and in many cases have low expectations to begin with. (Rightfully so, the female body is generally a lot harder to bring to sexual climax than the male body, and young men in particular are usually very poorly informed on the finer points, which gets compounded when their partner doesn't tell them what's working, and what isn't)
Further, particularly with the religious in many cases, they've been taught that "good girls don't like sex" so even if they DO know what good sex is. Because they've had good sex, they're then filled with self-loathing because they liked it. Which then creates all kinds of nasty when they then start avoiding it, even though they want more of it.
So when you do finally end up with a sexually active woman who knows what good sex is. Doesn't loathe herself for having and enjoying sex, and is willing to pursue more of it, just like their male counterparts. Why is it that she is the one who is the "slut" while the male is simply "normal" in doing the same thing from the other side?
While some versions of the NiS Stories do have indications that it may be trying to turn them into naked sex-addicts, most of them seem to be more on the order of discovering sex, and discovering that they enjoy it, and that they don't need to be ashamed of their enjoying it. That's healthy enough, and practically every NiS story seems to stop right about there, at least for the main characters. Now other students may run afoul of the Federal NiS types and end up closer to the Sex-Addict side of things, if they're lucky. But those are the stories they play into the grand conspiracy of NiS being a means for human sex-trafficking.
3] The stories ignore the difference between girls and boys to some extent. Especially, the Program officials seem to oblivious to the differences.
I'm not quite sure what you mean by this. The NiS Program, in particular the Wagner version of it, seems to go to great lengths to play up the "separate, but equal" political construct played out in an overtly sexual context. They point out the differences, and they play them up, usually to the detriment of the female student(unless they're truly (hyper-sexual) exhibitionists to start with, or just otherwise highly mentally resilient).